RetrogeneDB ID: retro_tbel_354

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1865:130734..131497(-)
• Located in intron of: ENSTBEG00000004092

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1A1
• Ensembl ID: ENSTBEG00000012151
• Aliases: None
• Description: eukaryotic translation elongation factor 1 alpha 1 [Source:HGNC Symbol;Acc:3189]

Sequence

>retro_tbel_354
AGTCAGAAGACATACGAGGAAATAGTGAGGGAAGTCAGCAGCTGCATTAAGAAAATTGGCACCAATCCTGGGACAGTAGC
ATTTCTTCCAACTTCTGGTTGGAATGGTGACAGCATGATAGAGCCAAGTGCTAACATGCCTTGGTTCAAGGGATGGAAAG
TCACCTACAAAGAATGTGAGACCAATGGAACCACACTGCTTGAAGCTCTGGATTGGATCCTGCCACCAACTCGTCCAACT
GACAAGCCCTTGCATCTGCCCCTCTAGGATGTGTACACTATCGGTGGTATTGACACTGTCCCTGTGGGCCGAGTGGAGAC
TGGTGTGCTCAAACCTGGTATGGTGGTCACCTTTGCACCAGTGAATGTGACAACTGAAGTAGAATCTGTTGAAAGGCACC
ATGAAGCTTTGAATGAAGCTCTTCCTGGGGACAATGTAGGCTTCAATGTCATGAACAGCCTGATAACGACGTTCAGTTTG
GCAATGTTGCTGGTGACAGCAAAAATGACCCACCAGTGGAAGCAGCTGTCTTCACTGCTCAGGTGATTATCCTGAACCAT
CCAGGCCAAATCAGCACTGGCTACGCCCTGTACTGGGTTGTCAAGCCCACATTGCTTGCAAGTTTGCTGAACCGAAGGAA
AAGATTGATTGCCATTCTGGTAAAAAGCTGGAAGGTGGCCCTAAATTCTTGAAATCTGGTGATGCTGCCATCATTGAAAT
GGTTCCCAGCAAGCCCATGTGTGTTGGGAGCTTCTCTGACTAT

Alignment

ORF - retro_tbel_354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.78 %
• Parental protein coverage: 55.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPWFKGWKVTRKDGNASGTTLLEAL
          SQK.YEEIV.EVS..IKKIG.NP.TVAF.P.SGWNGD.M.EPSANMPWFKGWKVT.K.....GTTLLEAL
Retrocopy SQKTYEEIVREVSSCIKKIGTNPGTVAFLPTSGWNGDSMIEPSANMPWFKGWKVTYKECETNGTTLLEAL

Parental  DCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPVNVTTEVKSVEMHHEALSEA
          D.ILPPTRPTDKPL.LPL.DVY.IGGI.TVPVGRVETGVLKPGMVVTFAPVNVTTEV.SVE.HHEAL.EA
Retrocopy DWILPPTRPTDKPLHLPL*DVYTIGGIDTVPVGRVETGVLKPGMVVTFAPVNVTTEVESVERHHEALNEA

Parental  LPGDNVGFNVKNVSV-KDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYA-PVLDCHTAHIAC
          LPGDNVGFNV.N.....DV..GNVAGDSKNDPP.EAA.FTAQVIILNHPGQIS.GYA.PVL.C..AHIAC
Retrocopy LPGDNVGFNVMNSLI<NDVQFGNVAGDSKNDPPVEAAVFTAQVIILNHPGQISTGYA<PVLGCQ-AHIAC

Parental  KFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDY
          KFAE.KEKID..SGKKLE.GPKFLKSGDAAI..MVP.KPMCV.SFSDY
Retrocopy KFAEPKEKIDCHSGKKLEGGPKFLKSGDAAIIEMVPSKPMCVGSFSDY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_354 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_354 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 121 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Echinops telfairi	ENSETEG00000004236	14 retrocopies	retro_etel_1189, retro_etel_1248, retro_etel_1260, retro_etel_1429, retro_etel_1436, retro_etel_1472, retro_etel_1578, retro_etel_1602, retro_etel_1682, retro_etel_1808, retro_etel_2135, retro_etel_366, retro_etel_411, retro_etel_830,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Microcebus murinus	ENSMICG00000015319	21 retrocopies	retro_mmur_1027, retro_mmur_1116, retro_mmur_1145, retro_mmur_1182, retro_mmur_1190, retro_mmur_12, retro_mmur_1282, retro_mmur_1316, retro_mmur_1339, retro_mmur_1343, retro_mmur_1350, retro_mmur_1568, retro_mmur_171, retro_mmur_26, retro_mmur_273, retro_mmur_49, retro_mmur_682, retro_mmur_729, retro_mmur_825, retro_mmur_877, retro_mmur_9,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Otolemur garnettii	ENSOGAG00000009152	10 retrocopies	retro_ogar_1215, retro_ogar_1622, retro_ogar_1779, retro_ogar_1840, retro_ogar_2281, retro_ogar_2526, retro_ogar_2557, retro_ogar_3013, retro_ogar_3046, retro_ogar_3271,
Pongo abelii	ENSPPYG00000016777	1 retrocopy	retro_pabe_12,
Tupaia belangeri	ENSTBEG00000012151	51 retrocopies	retro_tbel_1084, retro_tbel_1330, retro_tbel_1373, retro_tbel_1452, retro_tbel_166, retro_tbel_1841, retro_tbel_1969, retro_tbel_1994, retro_tbel_2088, retro_tbel_2091, retro_tbel_2179, retro_tbel_2205, retro_tbel_2206, retro_tbel_2218, retro_tbel_2232, retro_tbel_2419, retro_tbel_2505, retro_tbel_259, retro_tbel_2627, retro_tbel_2718, retro_tbel_2738, retro_tbel_2758, retro_tbel_282, retro_tbel_2976, retro_tbel_3032, retro_tbel_3065, retro_tbel_3067, retro_tbel_3281, retro_tbel_3307, retro_tbel_3315, retro_tbel_338, retro_tbel_354 , retro_tbel_360, retro_tbel_372, retro_tbel_3813, retro_tbel_3865, retro_tbel_3967, retro_tbel_4125, retro_tbel_4192, retro_tbel_4282, retro_tbel_4352, retro_tbel_4370, retro_tbel_4466, retro_tbel_4496, retro_tbel_4639, retro_tbel_4660, retro_tbel_4695, retro_tbel_473, retro_tbel_588, retro_tbel_620, retro_tbel_903,
Tupaia belangeri	ENSTBEG00000017170	16 retrocopies	retro_tbel_1335, retro_tbel_1406, retro_tbel_2677, retro_tbel_2899, retro_tbel_2966, retro_tbel_3336, retro_tbel_348, retro_tbel_3485, retro_tbel_3658, retro_tbel_3727, retro_tbel_3948, retro_tbel_4091, retro_tbel_4127, retro_tbel_4290, retro_tbel_4507, retro_tbel_4527,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,