RetrogeneDB ID: retro_btau_1497

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:72503152..72504551(-)
• Located in intron of: ENSBTAG00000014913

Retrocopy information

• Ensembl ID: ENSBTAG00000022199
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF2S3
• Ensembl ID: ENSBTAG00000014337
• Aliases: None
• Description: Eukaryotic translation initiation factor 2 subunit 3 [Source:UniProtKB/Swiss-Prot;Acc:Q2KHU8]

Sequence

>retro_btau_1497
GGGGGCGAGGCTGGTGTGACTTTAGGGCAGCCGCACCTTTCTCGGCAAGATCTCGCCACTTTGGATGTTTCCAAGTTGAC
GCCACTTTCACATGAAGTTATCAGCAGACAAGCCACAATTAATATAGGTACAATTGGTCACGTAGCTCATGGGAAATCTA
CAGTTGTAAAAGCTATTTCTGGAGTCCACACTGTCCGTTTCAAAAATGAACTGGAAAGAAATATTACAATCAAACTTGGC
TATGCTAATGCTAAGATTTATAAACTTGATGACCCAAGTTGTCCTCGGCCAGAATGTTATAGATCCTGTGGAAGTATCAC
ACCTGATGAGTTTCCTACAGACATTCCAGGGACCAAAGGGAACTTCAAATTAGTCAGGCATGTTTCCTTTGTTGACTGTC
CTGGCCATGATATTCTGATGGCTACTATGCTGAACGGTGTCGCAGTGATGGATGCCGCTCTTCTGTTGATAGCGGGTAAC
GAGTCTTGTCCTCAGCCTCAGACATCTGAACACTTGGCTGCTATAGAAATCATGAAACTGAAGCATATTTTGATTCTACA
AAATAAAATTGATTTGGTAAAAGAAAGCCAGGCTAAAGAACAGTATGAACAGATCCTTGCATTTGTTTGGTACAGTAGCA
GAAGGTGCTCCTATTATCCCAATTTCTGCTCAGCTAAAATACAATATTGAAGTTGTCTGTGAGTACATAGTAAAGAAAAT
TCCAGTACCCCCAAGAGACTTTACTTCAGAACCCAGACTTATTGTTATTAGATCCTTTGATGTCAACAAACCTGGCTGTG
AAGTTGATGACCTTAAGGGGGGTGTAGCTGGTGGTAGTATTCTAAAAGGAGTATTAAAGGTGGGCCAGGAGATAGAAGTC
AGACCTGGTATTGTTTCCAAAGACAGTGAAGGAAAACTCATGTGTAAACCTATCTTTTCCAAAATTGTATCGCTTTTCGC
AGAGCATTATGATCTTCAGTATGCTGCCCCAGGAGGTCTTATTGGAGTTGGAACAAAAATTGACCCCACTTTGTGCCGGG
CTGACAGAATGGTGGGGCAAGTACTTGGTGCGGTTGGAGCTTTACCTGAGATCTTCACAGAATTGGAAATTTCCTATTTC
CTGCTTAGAAGGCTTCTAGGTGTTCGCACTGAAGGAGACAAGAAAGCAGCGAAAGTACAAAAGCTGTCTAAGAATGAAGT
GCTTATGGTGAATATAGGATCCCTGTCGACAGGAGGAAGAGTTAGTGCAGTCAAGGCTGATTTGGGTAAAATCGTCTTGA
CTAATTCTGTGTGCACAGAAGTAGGAGAAAAGATTGCACTTAGCCGAAGAGGTGAGAAACACTGGCGTTTAATTGGTTGG
GGTCAAATAAGAAGAGGAGTGACAATCAAGCCGACAGTA

Alignment

ORF - retro_btau_1497 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.73 %
• Parental protein coverage: 98.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGEAGVTLGQPHLSRQDLATLDVSKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNE
          GGEAGVTLGQPHLSRQDLATLDVSKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNE
Retrocopy GGEAGVTLGQPHLSRQDLATLDVSKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNE

Parental  LERNITIKLGYANAKIYKLDDPSCPRPECYRSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILM
          LERNITIKLGYANAKIYKLDDPSCPRPECYRSCGS.TPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILM
Retrocopy LERNITIKLGYANAKIYKLDDPSCPRPECYRSCGSITPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILM

Parental  ATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLV-KESQAKEQYEQILAFV
          ATMLNG.AVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLV.K....K......L...
Retrocopy ATMLNGVAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLV>KKARLKNSMNRSLHLF

Parental  QGTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGG
          .GTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGG
Retrocopy -GTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGG

Parental  SILKGVLKVGQEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRAD
          SILKGVLKVGQEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEH.DLQYAAPGGLIGVGTKIDPTLCRAD
Retrocopy SILKGVLKVGQEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHYDLQYAAPGGLIGVGTKIDPTLCRAD

Parental  RMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVK
          RMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVK
Retrocopy RMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVK

Parental  ADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTV
          ADLGKIVLTN.VCTEVGEKIALSRR.EKHWRLIGWGQIRRGVTIKPTV
Retrocopy ADLGKIVLTNSVCTEVGEKIALSRRGEKHWRLIGWGQIRRGVTIKPTV

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
ERP005899_liver	0.07 RPM	45.13 RPM
ERP005899_muscle	0.63 RPM	146.60 RPM
SRP017611_brain	0.23 RPM	19.05 RPM
SRP017611_kidney	0.06 RPM	42.73 RPM
SRP017611_liver	0.23 RPM	24.16 RPM
SRP030211_testis	0.51 RPM	14.34 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1497 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1497 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1497 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014337	1 retrocopy	retro_btau_1497 ,
Dasypus novemcinctus	ENSDNOG00000018584	1 retrocopy	retro_dnov_1454,
Equus caballus	ENSECAG00000017343	1 retrocopy	retro_ecab_810,
Echinops telfairi	ENSETEG00000000341	4 retrocopies	retro_etel_1061, retro_etel_126, retro_etel_1590, retro_etel_2017,
Loxodonta africana	ENSLAFG00000011052	1 retrocopy	retro_lafr_971,
Macaca mulatta	ENSMMUG00000006979	4 retrocopies	retro_mmul_1965, retro_mmul_2258, retro_mmul_473, retro_mmul_713,
Monodelphis domestica	ENSMODG00000007541	2 retrocopies	retro_mdom_1650, retro_mdom_732,
Mus musculus	ENSMUSG00000035150	2 retrocopies	retro_mmus_1408, retro_mmus_3433,
Pongo abelii	ENSPPYG00000020194	1 retrocopy	retro_pabe_10,
Pteropus vampyrus	ENSPVAG00000002533	1 retrocopy	retro_pvam_936,
Sus scrofa	ENSSSCG00000012178	1 retrocopy	retro_sscr_805,
Ictidomys tridecemlineatus	ENSSTOG00000007144	1 retrocopy	retro_itri_582,
Tursiops truncatus	ENSTTRG00000012474	4 retrocopies	retro_ttru_1080, retro_ttru_1638, retro_ttru_617, retro_ttru_686,