RetrogeneDB ID: retro_ecab_586

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 22:8247489..8249256(+)
• Located in intron of: ENSECAG00000007559

Retrocopy information

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

Parental gene information

• Parental gene symbol: SENP2
• Ensembl ID: ENSECAG00000011230
• Aliases: None
• Description: SUMO1/sentrin/SMT3 specific peptidase 2 [Source:HGNC Symbol;Acc:23116]

Sequence

>retro_ecab_586
ATGTACAAATGGCTGGTTAGGATTCTCGGCACCATTTTCCGTCTCTGTGACCGGCCGGTGCCCCCTGCCCGGGCCCTCCT
GAAGAGGTGGCGCTCGAACAGCACTCTGTTGTCTACAGTGGACACTGATGAAATACCAGCCAAAAGACCAAGATTAGATT
GTTTTATTCACCAAGTGAAAACCAGTCTCTACAATGCTGCCGGCTTATTTGGATTCCCATTCCAGCTGAACACAAAGCCC
ATGGTAACTGCTGCTTGTAATGGAACACGGAATGTGGCCCCTTCAGAAGAGGTATTTTCAAACTCCTCATCTTGTGAACT
GACAGGTTCTGGATCCTGGAACAACATGCTGAAACTGGGTAATAAATCTCCTAATGGAATAAGTGACTATCCAGAGATCA
GAGTGATAGTAACCCGAGATCAGCCTCGCAGAGTCCTGCCTTCCTTTGGTTTTACCTTGAACTCAGAAGGCTATAATAGA
AGACCCGGTGGCCGTTGCCATAGCAAAAGCAATCCAGAGAGTTCCTTAACGTGGAAACCTCAAGAGCAGGTTGTAACAGA
GATGATCTCTGAAGAGGGTGGCAAGGGTCTGAGGCGTCCCCATTGTACAGTGGAGGAGGGTGTTCAAAAAGAGGAAAGAG
AGAAGTACTGGAGGTTATTGGAGCGACTTAAAGAAGGTGGTCATGGAAACACTGTTCCTCCTGTAACTTCAGCACATCAT
AGTTCTCAAAGAAGTCGCACGGACTCATTAAAGACCAAAGGCTGGGGGGAAGAGCAAAGTCACAGAGTCAAAACAGCTTA
GTTTGTTCCAAAATCATATAGAGTTGTTGAAACAAGGGGACCTCTGTGTTCTGTGAGAAGTGAAAAGAGATGTTCAAAGG
GGAAAATTTCTGATATAGAGAAGACAGTTGGAATCAGACTCGAAAATGAAGGTAGGAGAGGACACCAGCTGGAACCTGAC
CTGTCTGAAGAAGTGTCAGCCTGGCTCCGCCTAGGCAGTGGAAGCAATGGCTTACTCAGGAGGAAGATGTCAATACTTGA
GACTAAAGAGAAAAATTGCTCAGGCAGAGACAGGGATAAGAGGACGGATGATCTTCTTGAACTTACAGAGGACATGGAAA
AGGAAATCAGTAATGCCCTAGGCCATGGCCCTCAGGATGAGATTCTAAGTAGCGCTTTCAAACTCCGAATCACTCGAGGA
GATATCCAGACCTTGAAGAACTATCACTGGCTCAATGACGAAGTCATTAATTTTTACATGAATCTTCTGGTGGAAAGAAA
TAAAAAACAAGGGTATCCAGCACTTCATGCATTCAGTACTTTCTTCTATCCCAAATTAAAGTCTGGGGGTTACCAAGCAG
TGAAAAGATGGACCAAAGGGGTCAATCTCTTTGAACAGGAACTTATTCTGGTGCCTATTCATCGGAAGGTACATTGGAGC
CTGGTGGTGATAGACCTAAGAAAAAAGTGTCTTAAATATCTGGATTCTATGGGACAAAAGGGCCATAGGATCTGTGAGAT
TCTCCTTCAGTATTTACAGGAGGAAAGTAAGACCAAAAGAAATATTGATCCGAATCTTTTAGAGTGGACCCACTACAGCA
TGAAGCCACATGAGATTCCTCAACAGGTGAATGGGAGTGATTGTGGAATGTTTACTTGTAAATATGCAGATTATATCTCT
AGGGACAAACCTATCACATTTACTCAGCACCAGATGCCTCTCTTCCGGAAGAAGATGGTGTGGGAAATCCTTCATCAGCA
GTTACTG

Alignment

ORF - retro_ecab_586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYKWLVRILGTIFRLCDRPVPPARALLKRRRSNSTLLSTVDTDEIPAKRPRLDCFIHQVKTSLYNAASLF
          MYKWLVRILGTIFRLCDRPVPPARALLKR.RSNSTLLSTVDTDEIPAKRPRLDCFIHQVKTSLYNAA.LF
Retrocopy MYKWLVRILGTIFRLCDRPVPPARALLKRWRSNSTLLSTVDTDEIPAKRPRLDCFIHQVKTSLYNAAGLF

Parental  GFPFQLNTKPMVTAACNGTRNVAPSEEVFSNSSSCELTGSGSWNNMLKLGNKSPNGISDYPKIRVTVTRD
          GFPFQLNTKPMVTAACNGTRNVAPSEEVFSNSSSCELTGSGSWNNMLKLGNKSPNGISDYP.IRV.VTRD
Retrocopy GFPFQLNTKPMVTAACNGTRNVAPSEEVFSNSSSCELTGSGSWNNMLKLGNKSPNGISDYPEIRVIVTRD

Parental  QPRRVLPSFGFTLNSEGYNRRPGGRRHSKSNPESSLTWKPQEQVVTEMISEEGGKGLRRPHCTVEEGVQK
          QPRRVLPSFGFTLNSEGYNRRPGGR.HSKSNPESSLTWKPQEQVVTEMISEEGGKGLRRPHCTVEEGVQK
Retrocopy QPRRVLPSFGFTLNSEGYNRRPGGRCHSKSNPESSLTWKPQEQVVTEMISEEGGKGLRRPHCTVEEGVQK

Parental  EEREKYRRLLERLKEGGHGNTVPPVTSAHHSSQRSHTDTLKTKGWGEEQSHGVKTAQFVPKPYRVVETRG
          EEREKY.RLLERLKEGGHGNTVPPVTSAHHSSQRS.TD.LKTKGWGEEQSH.VKTA.FVPK.YRVVETRG
Retrocopy EEREKYWRLLERLKEGGHGNTVPPVTSAHHSSQRSRTDSLKTKGWGEEQSHRVKTA*FVPKSYRVVETRG

Parental  PLCSVRSEKRCSKGKISDIEKTVGIRLENEGRRGHQLEPDLSEEVSARLRLGSGSNGLLRRKMSILETKE
          PLCSVRSEKRCSKGKISDIEKTVGIRLENEGRRGHQLEPDLSEEVSA.LRLGSGSNGLLRRKMSILETKE
Retrocopy PLCSVRSEKRCSKGKISDIEKTVGIRLENEGRRGHQLEPDLSEEVSAWLRLGSGSNGLLRRKMSILETKE

Parental  KNCSGRDRDKRTDDLLELTEDMEKEISNALGHGPQDEILSSAFKLRITRGDIQTLKNYHWLNDEVINFYM
          KNCSGRDRDKRTDDLLELTEDMEKEISNALGHGPQDEILSSAFKLRITRGDIQTLKNYHWLNDEVINFYM
Retrocopy KNCSGRDRDKRTDDLLELTEDMEKEISNALGHGPQDEILSSAFKLRITRGDIQTLKNYHWLNDEVINFYM

Parental  NLLVERNKKQGYPALHAFSTFFYPKLKSGGYQAVKRWTKGVNLFEQELILVPIHRKVHWSLVVIDLRKKC
          NLLVERNKKQGYPALHAFSTFFYPKLKSGGYQAVKRWTKGVNLFEQELILVPIHRKVHWSLVVIDLRKKC
Retrocopy NLLVERNKKQGYPALHAFSTFFYPKLKSGGYQAVKRWTKGVNLFEQELILVPIHRKVHWSLVVIDLRKKC

Parental  LKYLDSMGQKGHRICELLLQYLQDESKTKRNIDLNLLEWTHYSMKPHEIPQQLNGSDCGMFTCKYADYIS
          LKYLDSMGQKGHRICE.LLQYLQ.ESKTKRNID.NLLEWTHYSMKPHEIPQQ.NGSDCGMFTCKYADYIS
Retrocopy LKYLDSMGQKGHRICEILLQYLQEESKTKRNIDPNLLEWTHYSMKPHEIPQQVNGSDCGMFTCKYADYIS

Parental  RDKPITFTQHQMPLFRKKMVWEILHQQLL
          RDKPITFTQHQMPLFRKKMVWEILHQQLL
Retrocopy RDKPITFTQHQMPLFRKKMVWEILHQQLL

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
SRP021940_articular_cartilage	0.06 RPM	5.25 RPM
SRP021940_cerebellum	0.00 RPM	6.80 RPM
SRP021940_embryo	0.20 RPM	8.87 RPM
SRP021940_placental_villous	0.05 RPM	6.01 RPM
SRP021940_synovial_membrane	0.11 RPM	3.90 RPM
SRP021940_testis	0.90 RPM	49.24 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_586 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_586 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_586 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011230	1 retrocopy	retro_ecab_586 ,
Rattus norvegicus	ENSRNOG00000001773	1 retrocopy	retro_rnor_1568,
Tursiops truncatus	ENSTTRG00000008239	1 retrocopy	retro_ttru_377,