RetrogeneDB ID: retro_ecab_140

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:117880136..117881438(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NADK
• Ensembl ID: ENSECAG00000022883
• Aliases: None
• Description: NAD kinase [Source:HGNC Symbol;Acc:29831]

Sequence

>retro_ecab_140
ATGGAAGTGGAACAAGAGAAAGTCAACATGAGTAAGGAGCTGAGTGCAGATGCGGCCTCGTACCGCTGCTCCGCGTGTCA
TGGGGACGAGGACTGGGGGCTCAGCCACCCCCATGCGGGGGCGGGCCAAGTCCCGCAGCTTGTCTGCCGCGCTGGCCCTG
GCAAGCACCAAGGAGTTCAGGAGGACCCGCTCCCTGCACAGGCCGTGCCCAGTGACCACTTTTGGACCAAAGGCCTGCGT
GCTGCAGAACCCCCAGACCATCATGCACATCCAGGACCCTGCTAGCCAGTGGTTGACGTGGAACAAGTCCCCAAAGAGTG
TTCTCGTCATCAAGAAGATCCGTGACGCCAGCCTGCCCCAGCCCTTCAAGGAGCTCTGCATGTACCTGATGGAGGAGAAC
AACATGATTGTGTATGTGGAGAAGAAAGTTCTAGAAGACCCTGCCATAGTGAGTGACGACAGCTTTGGGCCAGTGAAGAG
GAAGTTCTGCACCTTCAGAGAAGATTATGACGACATCTCCAATCAGATCGACCTCATCATCTGCCTGGGTGGGGACGGGA
CCCTGCTCTACGCCTCCTCCCTCTTCTCGGGCAGCGTGCCTCGGGTCATGGCTTTTCACCTGGCCTCCCTGGGCTTCCTG
ACCCCCTTCAACTTTGAGAACTTTCAGTCCCAAGATACTCAGGTGATACAGGGGAATGCAGCTGTTGTTCTTCGGAGCCG
GCTGAAGGTCAGGGTCGTGAAGGAGCTTAGAGGGAAGATGGCCATCCCCAACGGGATCAGCGAGAACGGGGTGCTGGCTG
CAGACCTGGACACAGAGGTCGGGAAGCAGGTCATGCAGTACCAGGTCTTGAATGAGGTGTTGATCGACTGAGGTCCGTCC
TCGTACCTGTCCAACGTGGACGTCTACCTGGACGGGCACCTCATCACCACGGTGCAGGGCGACGGGGTGATTGTGTCCAC
CCCGACGGGCAGCACAGCGTATGCGGCGACAGCGGGGCCTCCATGATCCACCCCAACGTGCCAGCCATCATGATCACACC
TATCTGCCCCCACTCACTGTCATTCCGGCCCATCGTGGTCCCTGCGGGGGTCGAGCTGAAGATCATGCTATCACCGGAAG
CTAGAAACACCGCCTGGGTGTCCTTTGATGGACGAAAGAGACAGGAGATCCGCCGCGGAGACAGCATCAGCATTGCTACC
TCTTGCTACCCCGTGCCCTCCATCAGCGTCCGAGACCCCATGAGCAACTGGTTTGAGAGCTTGGCTCAGTGTCTGCACTG
GAACGTGCGGAAGAAGCAGGCC

Alignment

ORF - retro_ecab_140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEVEQEKVNMSKELSADAASYRCSACHGDEDWGLSHP-MRGRAKSRSLSAAPAPASTKEFRRTRSLHGPC
          MEVEQEKVNMSKELSADAASYRCSACHGDEDWGLSHP.MRGRAKSRSLSAA.A.ASTKEFRRTRSLH.PC
Retrocopy MEVEQEKVNMSKELSADAASYRCSACHGDEDWGLSHP>MRGRAKSRSLSAALALASTKEFRRTRSLHRPC

Parental  PVTTFGPKACVLQNPQTIMHIQDPASQRLTWNKSPKSVLVIKKIRDASLLQPFKELCMYLMEENNMIVYV
          PVTTFGPKACVLQNPQTIMHIQDPASQ.LTWNKSPKSVLVIKKIRDASL.QPFKELCMYLMEENNMIVYV
Retrocopy PVTTFGPKACVLQNPQTIMHIQDPASQWLTWNKSPKSVLVIKKIRDASLPQPFKELCMYLMEENNMIVYV

Parental  EKKVLEDPAIVSDDSFGPVKRKFCTFRE-YDDISNQIDLIICLGGDGTLLYASSLFQGSVPPVMAFHLGS
          EKKVLEDPAIVSDDSFGPVKRKFCTFRE.YDDISNQIDLIICLGGDGTLLYASSLF.GSVP.VMAFHL.S
Retrocopy EKKVLEDPAIVSDDSFGPVKRKFCTFREDYDDISNQIDLIICLGGDGTLLYASSLFSGSVPRVMAFHLAS

Parental  LGFLTPFNFENFQSQVTQVIQGNAAVVLRSRLKVRVVKELRGKMAIPNGISENGVLATDLDTEVGKQVMQ
          LGFLTPFNFENFQSQ.TQVIQGNAAVVLRSRLKVRVVKELRGKMAIPNGISENGVLA.DLDTEVGKQVMQ
Retrocopy LGFLTPFNFENFQSQDTQVIQGNAAVVLRSRLKVRVVKELRGKMAIPNGISENGVLAADLDTEVGKQVMQ

Parental  YQVLNEVVIDRGPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAAAA-GASMIHPNVPAIMITPI
          YQVLNEV.ID.GPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAA.A.GASMIHPNVPAIMITPI
Retrocopy YQVLNEVLID*GPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAATA<GASMIHPNVPAIMITPI

Parental  CPHSLSFRPIVVPAGVELKIMLSPEARNTAWVSFDGRKRQEIRHGDSISITTSCYPLPSICVRDPVSDW-
          CPHSLSFRPIVVPAGVELKIMLSPEARNTAWVSFDGRKRQEIR.GDSISI.TSCYP.PSI.VRDP.S.W.
Retrocopy CPHSLSFRPIVVPAGVELKIMLSPEARNTAWVSFDGRKRQEIRRGDSISIATSCYPVPSISVRDPMSNWF

Parental  RAWLQCLHWNVRKKQA
          ....QCLHWNVRKKQA
Retrocopy ESLAQCLHWNVRKKQA

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	0.47 RPM	8.80 RPM
SRP021940_cerebellum	0.36 RPM	15.63 RPM
SRP021940_embryo	3.48 RPM	49.30 RPM
SRP021940_placental_villous	2.74 RPM	35.70 RPM
SRP021940_synovial_membrane	3.18 RPM	40.71 RPM
SRP021940_testis	7.23 RPM	50.77 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_140 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_140 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_140 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000022883	1 retrocopy	retro_ecab_140 ,
Ictidomys tridecemlineatus	ENSSTOG00000012783	1 retrocopy	retro_itri_511,