RetrogeneDB ID: retro_mdom_63

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:75570009..75572160(+)
• Located in intron of: ENSMODG00000004884

Retrocopy information

• Ensembl ID: ENSMODG00000004896
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000001962
• Aliases: None
• Description: None

Sequence

>retro_mdom_63
AGTCTCATGAACATTCATGGTTTTGATCTGGGCTCTCGGTATATGGACTTAAAACCACTGGGTTGTGGTGGCAATGGCTT
AGTTTTTTCTGCTGTCGATAATGACTGTGACAAAAGAGTGGCTGTCAAGAAAATTGTTCTTACAGATCCCCAGAGTGTTA
AACATGCTTTACGCGAAATCAAAATTATTAGAAGACTCGACCATGATAACATTGTGAAAGTATTTGAAATTCTTGGTCCC
AGTGGAAGCCAGTTAACAGATGATGTGGGCTCTCTGACAGAACTGAACAGTGTTTACATTGTTCAGGAGTACATGGAGAC
AGACTTGGCTAATCTGCTAGAGCAGGGCCCTTTATTGGAGGAGCATGCCAGGCTTTTCATGTATCAGCTGCTACGTGGGC
TCAAGTATATTCATTCTGCAAATGTACTGCACAGAGATCTCAAACCAGCTAATCTTTTCATTAATACCGAAGACTTGGTG
CTGAAGATAGGTGACTTTGGTCTTGCCCGGATCATGGATCCCCATTATTCCCACAAGGGTCATCTTTCTGAAGGATTGGT
TACTAAATGGTACAGATCTCCACGACTTTTACTTTCTCCTAATAACTATACTAAAGCCATTGATATGTGGGCTGCAGGAT
GCATCTTTGCTGAAATGCTGACTGGGAAAACCCTCTTTGCAGGTGCACATGAACTTGAACAGATGCAACTGATTTTAGAA
TCTATTCCTGTTGTACATGAGGAAGATCGTCAGGAGCTTCTCAGTGTAATCCCAGTTTACATAAAAAATGATATGACTGA
GCCACACAAACCCTTAACTCAGCTGCTTCCAGGAATTAGTCGTGAAGCACTGGACTTCCTGGAACAAATTTTGACATTTA
GTCCCATGGATCGATTGACCGCAGAAGAAGCTCTGTCCCATCCTTATATGAGCATTTATTCCTTTCCAATGGATGAACCA
ATTTCAAGCCATCCTTTTCACATTGAAGATGAAGTTGATGATATTTTGCTCATGGATGAAACTCATAGTCATATTTATAA
TTGGGAGAGGTACCATGATTGTCAGTTTTCAGACCATGACTGGCCTATACATAATAATTTTGATATTGAAGAAGTTCAGC
GTGACCCAAGGGCTCTTTCTGATGTCACTGATGAAGAGGAAGTCCAAGTAGATCCTCGAAAATATTTGGATGGAGATCGT
GAAAAGTATCTGAAGGATCCTGCCTTTGATACCCATTTCTCTACTGAGCCTTGTTGGCAATATCCAGATCATCATGAAAA
CAAGTATTGTGATCTGGAATGCAGCCACACTTGTAACTACAAAATGAGGTCGTCATCATATCTAGATAACTTAGTTTGGA
GAGAGAGTGAAGTTAACCATTACTATGAACCCAAACTTATTATAGATCTTTCTAATTGGAAAGAACAAAGCAAAGAAAAA
TCTGATAAGAAAGGCAAGTCAAAATGTGAAAGGAATGGATTGGTTAAAGCTCAAATAGCTCTTGAGGAAGCATCACAGCA
ACTGGTTGAAAAAGAAAGGGAGAAGAATCAAGGATTTGACTTTGATTCCTTTATTGCAGGAACTATTCAACTTAGTTCAC
AACATGAGTCTACTGATGTTGTTGATAAATTAAATGACTTGAATAGCTCAGTGTCCCAACTAGAATTGAAAAGTTTGATA
TCAAAGTCAGTAAGCCGGGAAAAACAGGAAAAAGGAATGGCGAATTTGGCTCAGTTAGAAGCTTTGTACCAGTCTTCTTG
GGACAGCCAGTTTGTGAGTGGTGGGGAGGAATGTTTTCTCATAGATCAGTTTTGTTGTGAAGTAAGAAAGGATGAACAGA
TTGAGAAGGAAAACACTTACACCAGTTACTTGGACAAGTTCTTTAGCAGGAAGGAAGATACTGAAATGCTAGAAACTGAG
CCAATAGAGGATGGCAAGTTTGGGGAAAGAGAAAGTGAGGAGGGTTTTCTTAACAATAGTGGGGAGTTCCTCTTTAACAA
GCAGCTTGAGTCTATAGGCATCCCACAGTTTCATAGTCCAGTTGGTTCACCACTTAAATCAATACAGGCTACATTAACAC
CTTCTGCTATGAAATCTTCCCCCCAGATTCCCCATAAAACATACAGCAGCATTCTGAAACATCTGAACTAA

Alignment

ORF - retro_mdom_63 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 99.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLMNIHGFDLGSRYMDLKPLGCGGNGLVFSAVDNDCDKRVAVKKIVLTDPQSVKHALREIKIIRRLDHDN
          SLMNIHGFDLGSRYMDLKPLGCGGNGLVFSAVDNDCDKRVAVKKIVLTDPQSVKHALREIKIIRRLDHDN
Retrocopy SLMNIHGFDLGSRYMDLKPLGCGGNGLVFSAVDNDCDKRVAVKKIVLTDPQSVKHALREIKIIRRLDHDN

Parental  IVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANLLEQGPLLEEHARLFMYQLLRGLKYIHSA
          IVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANLLEQGPLLEEHARLFMYQLLRGLKYIHSA
Retrocopy IVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANLLEQGPLLEEHARLFMYQLLRGLKYIHSA

Parental  NVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNYTKAIDMW
          NVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNYTKAIDMW
Retrocopy NVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNYTKAIDMW

Parental  AAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIKNDMTEPHKPLTQLLPGIS
          AAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIKNDMTEPHKPLTQLLPGIS
Retrocopy AAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIKNDMTEPHKPLTQLLPGIS

Parental  REALDFLEQILTFSPMDRLTAEEALSHPYMSIYSFPMDEPISSHPFHIEDEVDDILLMDETHSHIYNWER
          REALDFLEQILTFSPMDRLTAEEALSHPYMSIYSFPMDEPISSHPFHIEDEVDDILLMDETHSHIYNWER
Retrocopy REALDFLEQILTFSPMDRLTAEEALSHPYMSIYSFPMDEPISSHPFHIEDEVDDILLMDETHSHIYNWER

Parental  YHDCQFSDHDWPIHNNFDIEEVQRDPRALSDVTDEEEVQVDPRKYLDGDREKYLKDPAFDTHFSTEPCWQ
          YHDCQFSDHDWPIHNNFDIEEVQRDPRALSDVTDEEEVQVDPRKYLDGDREKYLKDPAFDTHFSTEPCWQ
Retrocopy YHDCQFSDHDWPIHNNFDIEEVQRDPRALSDVTDEEEVQVDPRKYLDGDREKYLKDPAFDTHFSTEPCWQ

Parental  YPDHHENKYCDLECSHTCNYKMRSSSYLDNLVWRESEVNHYYEPKLIIDLSNWKEQSKEKSDKKGKSKCE
          YPDHHENKYCDLECSHTCNYKMRSSSYLDNLVWRESEVNHYYEPKLIIDLSNWKEQSKEKSDKKGKSKCE
Retrocopy YPDHHENKYCDLECSHTCNYKMRSSSYLDNLVWRESEVNHYYEPKLIIDLSNWKEQSKEKSDKKGKSKCE

Parental  RNGLVKAQIALEEASQQLVEKEREKNQGFDFDSFIAGTIQLSSQHESTDVVDKLNDLNSSVSQLELKSLI
          RNGLVKAQIALEEASQQLVEKEREKNQGFDFDSFIAGTIQLSSQHESTDVVDKLNDLNSSVSQLELKSLI
Retrocopy RNGLVKAQIALEEASQQLVEKEREKNQGFDFDSFIAGTIQLSSQHESTDVVDKLNDLNSSVSQLELKSLI

Parental  SKSVSREKQEKGMANLAQLEALYQSSWDSQFVSGGEECFLIDQFCCEVRKDEQIEKENTYTSYLDKFFSR
          SKSVSREKQEKGMANLAQLEALYQSSWDSQFVSGGEECFLIDQFCCEVRKDEQIEKENTYTSYLDKFFSR
Retrocopy SKSVSREKQEKGMANLAQLEALYQSSWDSQFVSGGEECFLIDQFCCEVRKDEQIEKENTYTSYLDKFFSR

Parental  KEDTEMLETEPIEDGKFGERESEEGFLNNSGEFLFNKQLESIGIPQFHSPVGSPLKSIQATLTPSAMKSS
          KEDTEMLETEPIEDGKFGERESEEGFLNNSGEFLFNKQLESIGIPQFHSPVGSPLKSIQATLTPSAMKSS
Retrocopy KEDTEMLETEPIEDGKFGERESEEGFLNNSGEFLFNKQLESIGIPQFHSPVGSPLKSIQATLTPSAMKSS

Parental  PQIPHKTYSSILKHLN
          PQIPHKTYSSILKHLN
Retrocopy PQIPHKTYSSILKHLN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	14.30 RPM
SRP007412_cerebellum	0.00 RPM	12.73 RPM
SRP007412_heart	0.00 RPM	4.78 RPM
SRP007412_kidney	0.00 RPM	2.63 RPM
SRP007412_liver	0.00 RPM	9.57 RPM
SRP007412_testis	0.00 RPM	6.48 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_63 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_63 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000962	1 retrocopy	retro_cjac_2633,
Homo sapiens	ENSG00000069956	2 retrocopies	retro_hsap_1257, retro_hsap_2519,
Gorilla gorilla	ENSGGOG00000004003	1 retrocopy	retro_ggor_1571,
Monodelphis domestica	ENSMODG00000001962	2 retrocopies	retro_mdom_138, retro_mdom_63 ,
Monodelphis domestica	ENSMODG00000017722	1 retrocopy	retro_mdom_101,
Nomascus leucogenys	ENSNLEG00000006476	2 retrocopies	retro_nleu_1441, retro_nleu_2095,
Otolemur garnettii	ENSOGAG00000030786	1 retrocopy	retro_ogar_1827,
Pongo abelii	ENSPPYG00000006482	2 retrocopies	retro_pabe_1853, retro_pabe_3322,
Pan troglodytes	ENSPTRG00000020224	3 retrocopies	retro_ptro_1464, retro_ptro_2743, retro_ptro_3045,
Sarcophilus harrisii	ENSSHAG00000017091	1 retrocopy	retro_shar_445,
Sus scrofa	ENSSSCG00000004624	1 retrocopy	retro_sscr_162,
Tupaia belangeri	ENSTBEG00000007876	2 retrocopies	retro_tbel_1879, retro_tbel_2946,
Tursiops truncatus	ENSTTRG00000016253	2 retrocopies	retro_ttru_322, retro_ttru_75,