RetrogeneDB ID: retro_ecab_19

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:42306179..42307928(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000004701
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CSTF2
• Ensembl ID: ENSECAG00000009325
• Aliases: None
• Description: cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa [Source:HGNC Symbol;Acc:2484]

Sequence

>retro_ecab_19
GAGGTTGGTTCTGTTGTCAGTTTCCGGCTGGTATACGATCGAGAGACGGGAAAACCCAAGGGGTATGGCTTCTGCGAGTA
TCAAGACCAGGAGACCGCGCTTAGTGCCATGCGGAACCTTAATGGGCGGGAGTTCAGCGGGAGAGCGCTTCGGGTGGACA
ATGCTGCCAGTGAAAAGAACAAGGAGGAGTTAAAGAGCCTAGGGCCTGCAGCGCCCATCATTGACTCCCCCTACGGGGAC
CCCATCGATCCGGAAGATGCCCCAGAATCAATTACCAGGGCAGTTGCTAGTCTCCCCCCGGAGCAAATGTTTGAGCTGAT
GAAGCAGATGAAGCTGTGTGTCCAAAACAGTCACCAGGAAGCTCGAAACATGTTACTTCAAAACCCCCAACTGGCTTACG
CCCTGTTACAGGCGCAAGTAGTGATGAGGATCATGGATCCAGAGATTGCTTTGAAAATTCTGCATCGCAAGATACATGTC
ACACCGCTCATCCCAGGCAAATCTCAGCCTGTCTCTGGCCCTGGCCCTGGGATCTGCCCAGGACCTAATGTTCTACTGAA
CCAGCAGAATCCTCCAGCCCCTCAGCCTCAGCATTTGGCTAGAAGACCTGTGAAAGACATCCCTCCTCTGATGCAGACCC
CTATCCAGGGTGGAATTCCAGCCCCAGGGCCAATACCAACTGGGGTTCCCGGACCTGGTCCTGGTTCCTTAACTCCTGGT
GGAGCAATGCAGCCCCAAGTTGGAATGCCAGGGGTTGGTCCTGTGCCTTTAGAGCGGGGACAGGTGCAGATGTCGGATCC
TAGAGCTCCTATGCCTCGTGGACCCATGACTGCTGGTGGCCTGCCTCCTCGAGGACTGTTAGGAGATGCACCAAATGACC
CACGTGGAGGGACTTTGCTCTCAGTCACTGGAGAAGTAGAGCCCAGAGGCTATCTTGGCCCACCTCATCAGGGTCCCCCT
ATGCACCATGCCTCTGGTCATGACAGCCGTGGCCCTTCCTCACATGAGATGAGGGGAGGGCCATTAGCAGATCCCAGAAT
GCTAATTGGAGAGCCCAGAGGACCCATGATGGATCAAAGGGGTCTACCTTTGGATGGTAGAGGTAGTAGAGATTCTCGAG
GGATGGAGACTCGAGCCATGGAAACTGAGGTCTTAGAGACACGAGTAATGGAGAGAAGAGGAATGGAGACCTGTGCAATG
GAAGCCAGAGGGATGGAAGCAAGAGGCATGGATGCAAGAGGAATGGAGATAAGGGGCCCTGGCCCCAGTTCGAGAGGCCC
TATGACTGGTGGAATCCAGGGTCCTGGTCCCATTAATATGGGGGCAGGTGGTCCTCAGGGACCCAGACAGGTCCCAAGCA
TTTCAGGGGTGGGAAATCCTGGAGCTGGCATGCAGGGGGCAGGCATACAAGGAGCAGGCATGCAGGGAGCGGGCATGCAG
GGATCGGGCATGCAGGGAGCAGGCATGCAGGGAGCGGGCATGCAGGGAGCGGGCATACAAGGAGTGGGCATGCAGGGGGC
CGGCATACAAGGAACGGGCATGCAGGGGGCGGGCAAGCAAGGTGGAGGCCAGCCTAGCAGTTTTAGTCCTGGGCAGAGCC
AAGTAACTCCCCAGGATCAAGAAAAGGCAGCTTTGATCATGCAGGTTCTTCAACTGACTGCAGATCAGATTGCCATGCTG
CCTCCTGAGCAAAGGCAGAGCATCCTGATTTTAAAGGAACAAATCCAGAAGTCTACTGGAGCTTCTTGA

Alignment

ORF - retro_ecab_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.97 %
• Parental protein coverage: 84.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVGPVVSYLLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTG
          EVG.VVS..LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLG..
Retrocopy EVGSVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGPA

Parental  APVIESPYGETISPEDAPESISKAVASLPPEQMFELMKQMKLCVQNSPQEARNMLLQNPQLAYALLQAQV
          AP.I.SPYG..I.PEDAPESI..AVASLPPEQMFELMKQMKLCVQNS.QEARNMLLQNPQLAYALLQAQV
Retrocopy APIIDSPYGDPIDPEDAPESITRAVASLPPEQMFELMKQMKLCVQNSHQEARNMLLQNPQLAYALLQAQV

Parental  VMRIVDPEIALKILHRQTNIPTLIAGNPQPVHSTGPG--SGSNVSMNQQNPQAPQAQSLGGMHVNGAPPL
          VMRI.DPEIALKILHR......LI.G..QPV...GPG...G.NV..NQQNP.APQ.Q.L....V...PPL
Retrocopy VMRIMDPEIALKILHRKIHVTPLIPGKSQPVSGPGPGICPGPNVLLNQQNPPAPQPQHLARRPVKDIPPL

Parental  MQASMQAGVPTPGQMPASVTGPGPGALAPGGGMQAQVGMPGSGPVSMERGQVPMQDPRAAMQRGPLPANV
          MQ...Q.G.P.PG..P..V.GPGPG.L.PGG.MQ.QVGMPG.GPV..ERGQV.M.DPRA.M.RGP..A..
Retrocopy MQTPIQGGIPAPGPIPTGVPGPGPGSLTPGGAMQPQVGMPGVGPVPLERGQVQMSDPRAPMPRGPMTAGG

Parental  PTPRGLLGDAPNDPRGGTLLSVTGEVEPRGYLGPPHQGPPMHHVPGHDSRGPPPHEMRGGPLAEPRPLMA
          ..PRGLLGDAPNDPRGGTLLSVTGEVEPRGYLGPPHQGPPMHH..GHDSRGP..HEMRGGPLA.PR.L..
Retrocopy LPPRGLLGDAPNDPRGGTLLSVTGEVEPRGYLGPPHQGPPMHHASGHDSRGPSSHEMRGGPLADPRMLIG

Parental  EPRGPMLDQRGPPLDGRGGRDPRGMDARGMEARAMEARGLDARGLEARAMEARAMEARAMEARAMEARAM
          EPRGPM.DQRG.PLDGRG.RD.RGM..R.ME....E.R....RG.E..AMEAR.MEAR.M.AR.ME.R..
Retrocopy EPRGPMMDQRGLPLDGRGSRDSRGMETRAMETEVLETRVMERRGMETCAMEARGMEARGMDARGMEIRGP

Parental  EVRGMEARSMDTRGPVPGPRGPIPSGIQGPSPI-NMGAVG-PQGSRQVPVMQGAAMQGASIQGGGQPGGF
          .............GP..GP......G.QGP........VG.P....Q....QGA.MQGA..QG.G..G..
Retrocopy GPSSRGPMTGGIQGP--GPINMGAGGPQGPRQVPSISGVGNPGAGMQGAGIQGAGMQGAGMQGSGMQGAG

Parental  SPG
          ..G
Retrocopy MQG

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	29.46 RPM	5.25 RPM
SRP021940_cerebellum	43.26 RPM	12.57 RPM
SRP021940_embryo	65.08 RPM	16.95 RPM
SRP021940_placental_villous	20.50 RPM	10.83 RPM
SRP021940_synovial_membrane	24.30 RPM	10.05 RPM
SRP021940_testis	68.80 RPM	9.40 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_19 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_19 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_19 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000008257	1 retrocopy	retro_ecab_664,
Equus caballus	ENSECAG00000009325	1 retrocopy	retro_ecab_19 ,
Felis catus	ENSFCAG00000007000	1 retrocopy	retro_fcat_43,
Macropus eugenii	ENSMEUG00000011186	1 retrocopy	retro_meug_356,
Tursiops truncatus	ENSTTRG00000013556	1 retrocopy	retro_ttru_1363,