RetrogeneDB ID: retro_sscr_162

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:86131127..86132548(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK6
• Ensembl ID: ENSSSCG00000004624
• Aliases: MAPK6, SUSERK3
• Description: mitogen-activated protein kinase 6 [Source:HGNC Symbol;Acc:6879]

Sequence

>retro_sscr_162
CTCTCTGCAGGTGCACATGAACTTGAACAGATGCTGCTGATTTTAGAATCTTTTCCTGTTGTGCATGAGGAAGATCGTCA
GGAGCTTCTCAGTGTAATTCCAGTTTACATCAGAAATGATCTGACTGAGCCACACAAACCTTTAACTCAGCTGCTTCCAG
GAATTAGTCAAGAAGCACTGGATTTCCTGGAACAAATTTTGACATTTAGCCCCACTGATCGGTTGACGCAGAAGAAGCAC
TTTCCCATCCTTACATGAGCATTTATTCTTTTCCAATGGATAAGCCTATTTCAATTCATCCTTTTCATATTGAAGATGAT
GATGTTTTGCTTATGGATGAAACTCAGAGTCACATTTATAACTGGGAAAGGTACCATGATTGTCAATTTTCAGAGCATGA
ATGGCCTATACATAACAACTTTGATACTGATGAAGTTTATCTTGACCCAAGAGCTCTGTCTGATGTCACTGATGAAGAGG
AAGTACAAGTCAATCCTTGAAAATATTTGGATGGAGATCGTGAAAAGTATTTGGAGGATCTTGCTTTTGATACCAATTAC
TTGACTGAGCCTTGTTGGCAATACCCAGATCACCATGAAAACAAACATTGTGATCTGGAGTGTAGCCATACTTGTAACTA
CAAAACCAGGTCATCATCCTATTTAGATAACTTAGTTTGGAGAGAGAGTGAAGTTAATCATTACCATGAACCCAAGCTTA
TTATAGATCTTTCCAATTGGAAAGAACAAAGCAAAGAAAAATCTGATAAGAAAGGCAAGTCAAAATGTGAAAGGAATGGA
TTGGTTAAAGCCCAGATAGCCCTAGAGGAAGCATTACAGCAATTGGCTGAAAAAGAAAGGGAAAAGAATCAGGGATTTGA
CTTTGATTCCTTTATTGCAGGAACTATTCAACTTAGTTCACAACATGAGCCTACTGATGTTGTTGACAAATTAAATGACT
TGAATAGCTCAGCGTCCCAACTAGAATTGAAAAGTTTGATATCGAAGTCAGTAAGCTGAGAAAAACAGGAAAAAGGAACG
GCAAATTTGGCTCAGTTAGAAGCCTTGTACCGGTCTTCTTGGGATAGCCAGTTTGAGGGCGGTGGAGAGGACTGTTTTCT
CATGAATCAGTTTCGTTATGAGGTAAGGAAGGATGAGCAAATTGAAAAGGAAAGTACTTACACCAGTTACCTGGACAAGT
TCTTTAGCGGGAAACAAGATACTGAAATGCTAGAAACTGAGCCAGTAGAAGATGGGAAGCTTGGGGAGAGAGAAAATGAG
GAAGGATTTCTGGACAACAGTGGGGAGTTCCACCTTAATAAGCAACTTGAATCTATAGGCATCCCACAGTTTCACAGTGC
AGCTGGGTCACCACTTAAGTAAATACAGGCCACGTTAACACCTTCTGCTATGAAATCTTCC

Alignment

ORF - retro_sscr_162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.99 %
• Parental protein coverage: 65.93 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLTQLLPGISREALDFLEQILTFS
          L.AGAHELEQM.LILES.PVVHEEDRQELLSVIPVYIRND.TEPHKPLTQLLPGIS.EALDFLEQILTFS
Retrocopy LSAGAHELEQMLLILESFPVVHEEDRQELLSVIPVYIRNDLTEPHKPLTQLLPGISQEALDFLEQILTFS

Parental  PMDRLT-AEEALSHPYMSIYSFPMDEPISSHPFHIEDEVDDILLMDETHSHIYNWERYHDCQFSEHDWPI
          P.DRLT.AEEALSHPYMSIYSFPMD.PIS.HPFHIED..DD.LLMDET.SHIYNWERYHDCQFSEH.WPI
Retrocopy PTDRLT<AEEALSHPYMSIYSFPMDKPISIHPFHIED--DDVLLMDETQSHIYNWERYHDCQFSEHEWPI

Parental  HNNFDIDEVQLDPRALSDVTDEEEVQVDPRKYLDGDREKYLEDPAFDTNYSTEPCWQYPDHHENKYCDLE
          HNNFD.DEV.LDPRALSDVTDEEEVQV.P.KYLDGDREKYLED.AFDTNY.TEPCWQYPDHHENK.CDLE
Retrocopy HNNFDTDEVYLDPRALSDVTDEEEVQVNP*KYLDGDREKYLEDLAFDTNYLTEPCWQYPDHHENKHCDLE

Parental  CSHTCNYKTRSSSYLDNLVWRESEVNHYYEPKLIIDLSNWKEQSKEKSDKKGKSKCEKNGLVKAQIALEE
          CSHTCNYKTRSSSYLDNLVWRESEVNHY.EPKLIIDLSNWKEQSKEKSDKKGKSKCE.NGLVKAQIALEE
Retrocopy CSHTCNYKTRSSSYLDNLVWRESEVNHYHEPKLIIDLSNWKEQSKEKSDKKGKSKCERNGLVKAQIALEE

Parental  ASQQLAEKEREKNQGFDFDSFIAGTIQLSSQHEPTDVVDKLNDLNSSVSQLELKSLISKSVSREKQEKGK
          A.QQLAEKEREKNQGFDFDSFIAGTIQLSSQHEPTDVVDKLNDLNSS.SQLELKSLISKSVS.EKQEKG.
Retrocopy ALQQLAEKEREKNQGFDFDSFIAGTIQLSSQHEPTDVVDKLNDLNSSASQLELKSLISKSVS*EKQEKGT

Parental  ANLAQLEALYQSSWDSQFVGGGEDCFLINQFCCEVRKDEHIEKENNYTSYLDKFFSRKEDTEMLETEPVE
          ANLAQLEALY.SSWDSQF.GGGEDCFL.NQF..EVRKDE.IEKE..YTSYLDKFFS.K.DTEMLETEPVE
Retrocopy ANLAQLEALYRSSWDSQFEGGGEDCFLMNQFRYEVRKDEQIEKESTYTSYLDKFFSGKQDTEMLETEPVE

Parental  DGKLGERENEEGFLNNSGEFLFNKQLESIGIPQFHSPVGSPLKSIQATLTPSAMKSS
          DGKLGERENEEGFL.NSGEF..NKQLESIGIPQFHS..GSPLK.IQATLTPSAMKSS
Retrocopy DGKLGERENEEGFLDNSGEFHLNKQLESIGIPQFHSAAGSPLK*IQATLTPSAMKSS

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
SRP014902_placenta	0.00 RPM	18.58 RPM
SRP014902_testis	0.00 RPM	18.95 RPM
SRP018288_heart	0.03 RPM	77.01 RPM
SRP018288_kidney	0.20 RPM	126.28 RPM
SRP018288_liver	0.48 RPM	122.49 RPM
SRP018288_lung	0.10 RPM	48.88 RPM
SRP018856_adipose	0.06 RPM	23.90 RPM
SRP035408_brain	0.00 RPM	71.75 RPM
SRP035408_liver	0.03 RPM	205.61 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_162 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_162 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_162 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000001962	2 retrocopies	retro_mdom_138, retro_mdom_63,
Otolemur garnettii	ENSOGAG00000030786	1 retrocopy	retro_ogar_1827,
Sarcophilus harrisii	ENSSHAG00000017091	1 retrocopy	retro_shar_445,
Sus scrofa	ENSSSCG00000004624	1 retrocopy	retro_sscr_162 ,