RetrogeneDB ID: retro_mdom_1135

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:206375534..206376239(-)
• Located in intron of: ENSMODG00000020109

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CHPT1
• Ensembl ID: ENSMODG00000002564
• Aliases: None
• Description: choline phosphotransferase 1 [Source:HGNC Symbol;Acc:17852]

Sequence

>retro_mdom_1135
CAATGGCTGTTTTTCTGCTGTTTTGTTGGGATGTTTATGTTTTACTGTGCACACTGACAAATCTATGTATCTAGAGTGCT
ACGGTTTGGAAGAGTGGATGTAACTGAAGTACAGATAGCGATCACAATTGTCTTTTTTATAACTTCAATTGGAGGAACAA
TGATGTGGGATTATACTGTGATCAATTAAAACTGAAGATGTTACCTCTCATTGGGATACTGACAGGAGCATTTATTTCTT
GTTTTAATTATTTCCAAGTCATCCTTGGTGGAGGAGTTGGCAAGAATGGATCCACAACTGCAGGCACCAGTGTTTTGTCA
CCTGGCATCCACATAGGAGTAATTATTCTTCTAGCCATAATGATCCACAAAAAAATCTGCAACTCAGCTGTTTGAAAAAC
ATCCCTGTCTGTATATTTTAATGTTTGGGTGTGTGTATGCCAAAATCACACAAAAATTGGTGGTTGCTCACATGACCAAA
AGTAAACTAAAACTACAAGATTCTGCATTTATTGGTCCAGCTCTTCTGTTTTTTGATCAATACTTCAACCATGTTATAGA
TGAATATATTGTTCTGTGGGTACTAATGATCATCTCTTTATTTACTTCGCTGAAATATTTCATTACTGTGGTCGTGCAGA
TTGCAGATCACTTAAATTTACAAGTCTTCAGGATTCTACCTCCTCCAGCACCCGAACAGGTTCAA

Alignment

ORF - retro_mdom_1135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.05 %
• Parental protein coverage: 56.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EWLFFCCFVGMFMFYCAHWQTYVSGVLRFGRVDVTEVQIAITIVFFITAIGGTMMWDYTI-PVIQLKLKM
          .WLFFCCFVGMFMFYCAH.Q.YVS.VLRFGRVDVTEVQIAITIVFFIT.IGGTMMWDYT......LK...
Retrocopy QWLFFCCFVGMFMFYCAH*QIYVSRVLRFGRVDVTEVQIAITIVFFITSIGGTMMWDYTV<DQLKLKM--

Parental  LPLIGILTGAFISCFNYFQVILGGGVGKNGSTTAGTSVLSPGIHIGVIILLAIMIH-KKSATQLFEKHPC
          LPLIGILTGAFISCFNYFQVILGGGVGKNGSTTAGTSVLSPGIHIGVIILLAIMIH.KKSATQLFEKHPC
Retrocopy LPLIGILTGAFISCFNYFQVILGGGVGKNGSTTAGTSVLSPGIHIGVIILLAIMIH>KKSATQLFEKHPC

Parental  LYILMFGCVYAKITQKLVVAHMTKSKLKLQDSAFIGPALLFFDQYFNHVIDEYIVLWVAMIISLFTLLKY
          LYILMFGCVYAKITQKLVVAHMTKSKLKLQDSAFIGPALLFFDQYFNHVIDEYIVLWV.MIISLFT.LKY
Retrocopy LYILMFGCVYAKITQKLVVAHMTKSKLKLQDSAFIGPALLFFDQYFNHVIDEYIVLWVLMIISLFTSLKY

Parental  FITVVVQIADHLNLQVFRIPPPPAPVQVQ
          FITVVVQIADHLNLQVFRI.PPPAP.QVQ
Retrocopy FITVVVQIADHLNLQVFRILPPPAPEQVQ

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1135 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1135 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013377	1 retrocopy	retro_chof_712,
Loxodonta africana	ENSLAFG00000004678	1 retrocopy	retro_lafr_586,
Monodelphis domestica	ENSMODG00000002564	1 retrocopy	retro_mdom_1135 ,